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Information on EC 1.1.1.268 - 2-(R)-hydroxypropyl-CoM dehydrogenase
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EC Tree
1.1.1.268 2-(R)-hydroxypropyl-CoM dehydrogenaseIUBMB Comments
The enzyme is highly specific for (R)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (S)-enantiomer. This enzyme forms component III of a four-component enzyme system (comprising EC 4.4.1.23 [2-hydroxypropyl-CoM lyase; component I], EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV]) that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
r-hpcdh, (r)-hydroxypropyl-coenzyme m dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
(R)-hydroxypropyl-coenzyme M dehydrogenase
2-(2-(R)-hydroxypropylthio)ethanesulfonate dehydrogenase
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-
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2-(R)-hydroxypropyl-coenzyme M dehydrogenase
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-
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R-HPCDH
xecD
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
highly specific
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-
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2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
The enzyme is highly specific for (R)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (S)-enantiomer. This enzyme forms component III of a four-component enzyme system. Comprising EC 4.2.99.19, 2-hydroxypropyl-CoM lyase, component I, EC 1.8.1.5, 2-oxopropyl-CoM reductase, carboxylating, component II, EC 1.1.1.268, 2-(R)-hydroxypropyl-CoM dehydrogenase, component III, and EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, component IV, that is involved in epoxylalkane carboxylation in Xanthobacter sp. strain Py2
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2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
active site structure modeling and stereochemistry of reaction mechanism, overview
2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
active site structure modeling and stereochemistry of reaction mechanism, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
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redox reaction
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reduction
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-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
2-[2-(R)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase
The enzyme is highly specific for (R)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (S)-enantiomer. This enzyme forms component III of a four-component enzyme system (comprising EC 4.4.1.23 [2-hydroxypropyl-CoM lyase; component I], EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV]) that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
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CAS REGISTRY NUMBER
COMMENTARY
244301-33-5
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
(2S)-2-butanol + NAD+
2-butanone + NADH + H+
very low activity
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-
r
2-(2-hydroxyethylthio)ethanesulfonate + NAD+
2-(formylmethylthio)ethanesulfonate + NADH + H+
achiral mimic of both R-hydroxypropyl-CoM and S-hydroxypropyl-CoM, substrate for both the R- and S-HPCDH enzymes with identical Km values
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r
2-(2-hydroxyethylthio)ethanesulfonate + NADH + H+
?
very low activity
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-
?
2-(S)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
oxidation of S-hydroxypropyl-CoM with a kcat that is 402 times less than that for R-hydroxypropyl-CoM
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r
2-butanone + NADH + H+
(2R)-2-butanol + NAD+
with no additives present, all forms of recombinant R-HPCDH prefer a re-face hydride addition to produce an enantiomeric excess (EE) of (S)-2-butanol, S- and R-2-butanol are comparably good substrates for the reverse reaction. The sulfonate of ethanesulfonate interacts with R152 and R196 in the CoM binding pocket alongside 2-butanone, in a way that discourages a si-face hydride addition to produce (R)-2-butanol
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-
r
2-butanone + NADH + H+
(2S)-2-butanol + NAD+
with no additives present, all forms of recombinant R-HPCDH prefer a re-face hydride addition to produce an enantiomeric excess (EE) of (S)-2-butanol, S- and R-2-butanol are comparably good substrates for the reverse reaction. The sulfonate of ethanesulfonate interacts with R152 and R196 in the CoM binding pocket alongside 2-butanone, in a way that discourages a si-face hydride addition to produce (R)-2-butanol
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r
2-butanone + NADH + H+
(S)-2-butanol + (R)-2-butanol + NAD+
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without additions, 71.9% (S)-enantiomer + 28% (R)-enantiomer, in presence of 1 mM ethansulfonate 92.7% (S)-enantiomer + 7.3% (R)-enantiomer
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r
2-oxopropyl-CoM + NADH + H+
2-(R)-hydroxypropyl-CoM + NAD+
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r
2-[(R)-2-hydroxypropylthio]ethanesulfonate + NAD+
2-(2-ketopropylthio)ethanesulfonate + NADH + H+
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the enzyme is highly specific for the R-enantiomer
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r
2-[(S)-2-hydroxypropylthio]ethanesulfonate + NAD+
2-(2-ketopropylthio)ethanesulfonate + NADH + H+
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the enzyme is highly specific for the R-enantiomer
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r
(2R)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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r
(2R)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
substrate binding structure, overview
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r
(2R)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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r
(2R)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
substrate binding structure, overview
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r
(2S)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
competitive inhibitor to the R-enantiomer of substrate, very low activity
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r
(2S)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
competitive inhibitor to the R-enantiomer of substrate, very low activity
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r
(R)-2-butanol + NAD+
2-butanone + NADH + H+
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the enantiomeric selectivity of the reverse reaction is 39.6% for (S)-2-butanol without additive, 90.8% with 1 mM CH3CH2SO3-Na+ as additive, 87.8% with 1 mM HSCH2CH2SO3-Na+ as additive, 52.0% with 1 mM CH3CH2COO-Na+ as additive, 46.6% with 1 mM CH3COO-Na+ as additive, 44.8% with 1 mM CH3CH2NH3+Cl- as additive, 45.4% with 1 mM CH3CH2OH as additive, 45.8% with 1 mM Na2SO4 as additive and 40.4% with 1 mM NaCl as additive
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r
2-(2-hydroxyethylthio)ethanesulfonate + NAD+
2-(2-oxoethylthio)ethanesulfonate + NADH
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?
2-(2-hydroxyethylthio)ethanesulfonate + NAD+
2-(2-oxoethylthio)ethanesulfonate + NADH
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?
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH
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bacterial propylene metabolism
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?
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH
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bacterial propylene metabolism
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?
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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?
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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?
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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r
2-propanol + NAD+
2-propanone + NADH + H+
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r
additional information
?
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R-HPCDH1 can bind either enantiomer of hydroxypropyl-CoM with the CoM moiety oriented properly in the sulfonate-binding pocket consisting of R152 and R196. A high-affinity ternary complex of S-HPC, NAD+ forms, but the misalignment of the hydrogen and hydroxyl groups on C2 relative to NAD+ and the tyrosine general base results in a 403-fold lower turnover rate for the S-enantiomer
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?
additional information
?
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substrate specificity of the stereochemically different isozymes, R- and S-HPCDH (EC 1.1.1.269) are 41% identical to each other, overview. No activity with (S)-2-hexanol, (S)-2-heptanol, and (S)-2-octanol. Stereochemistry of products from reaction with wild-type and mutant enzymes with or without addition of additives, i.e. CH3CH2SO3- Na+, HSCH2CH2SO3- Na+, CH3CH2COO- Na+, CH3COO- Na+, CH3CH2NH3 +Cl-, CH3CH2OH, Na2SO4, and NaCl, overview
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additional information
?
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substrate specificity of the stereochemically different isozymes, R- and S-HPCDH (EC 1.1.1.269) are 41% identical to each other, overview. No activity with (S)-2-hexanol, (S)-2-heptanol, and (S)-2-octanol. Stereochemistry of products from reaction with wild-type and mutant enzymes with or without addition of additives, i.e. CH3CH2SO3- Na+, HSCH2CH2SO3- Na+, CH3CH2COO- Na+, CH3COO- Na+, CH3CH2NH3 +Cl-, CH3CH2OH, Na2SO4, and NaCl, overview
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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?
(2R)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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r
(2R)-2-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH + H+
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-
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r
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH
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bacterial propylene metabolism
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?
2-(R)-hydroxypropyl-CoM + NAD+
2-oxopropyl-CoM + NADH
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bacterial propylene metabolism
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?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-mercaptoethanesulfonate
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i.e. coenzyme M: function in catabolic pathway of hydrocarbon oxidation
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-(2-methyl-2-hydroxypropylthio)-ethanesulfonate
M-HPC, competitive inhibition
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2-bromoethanesulfonate
CoM-analogue, mixed type inhibitor. 32.7% residual activity at 5 mM, reversible inhibition
2-oxopropyl-CoM
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mixed-type inhibitor with respect to 2-(R)-hydroxypropyl-CoM
NADH
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mixed-type inhibitor with respect to 2-(R)-hydroxypropyl-CoM, competitive inhibition with respect to 2-oxopropyl-CoM
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
competitive
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
methanesulfonate
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1 mM, 5.6fold increase in ratio of turnover number to Km-value for 2-butanone as substrate
propanesulfonate
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1 mM, 1.7fold increase in ratio of turnover number to Km-value for 2-butanone as substrate
ethanesulfonate
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1 mM, 5.6fold increase in ratio of turnover number to Km-value for 2-butanone as substrate
ethanesulfonate
the addition of ethanesulfonate dramatically increases the enentiomeric excess of (S)-2-butanol produced by all forms of recombinant R-HPCDH except the R152A and R196A mutants. The effect of ethanesulfonate and other additives on (S)-butanol production is termed enantioselective modulation, and it is highly selective for sulfonate containing molecules. The interpretation is that the sulfonate of ethanesulfonate interacts with R152 and R196 in the CoM binding pocket alongside 2-butanone, in a way that discourages a si-face hydride addition to produce (R)-2-butanol
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
326
(2R)-2-butanol
recombinant enzyme, pH and temperature not specified in the publication
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2.64
(2R)-2-heptanol
recombinant enzyme, pH and temperature not specified in the publication
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4.6
(2R)-2-hexanol
recombinant enzyme, pH and temperature not specified in the publication
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0.102
(2R)-2-hydroxypropyl-CoM
recombinant enzyme, pH and temperature not specified in the publication
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1.08
(2R)-2-octanol
recombinant enzyme, pH and temperature not specified in the publication
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20
(2R)-2-pentanol
recombinant enzyme, pH and temperature not specified in the publication
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315
(2S)-2-butanol
recombinant enzyme, pH and temperature not specified in the publication
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0.1
(2S)-2-hydroxypropyl-CoM
recombinant enzyme, pH and temperature not specified in the publication
153
(2S)-2-pentanol
recombinant enzyme, pH and temperature not specified in the publication
-
additional information
additional information
steady-state kinetics, comparison of steady-state kinetics with wild-type an d mutant enzymes, overview
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0.75
2-(2-hydroxyethylthio)ethanesulfonate
recombinant enzyme, pH and temperature not specified in the publication
0.092
2-(2-ketopropylthio)ethanesulfonate
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pH 7.5, 30°C, wild-type enzyme
0.44
2-(2-ketopropylthio)ethanesulfonate
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pH 7.5, 30°C, mutant enzyme R209A
1726
2-propanol
recombinant enzyme, pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.98
(2R)-2-butanol
recombinant enzyme, pH and temperature not specified in the publication
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1.8
(2R)-2-heptanol
recombinant enzyme, pH and temperature not specified in the publication
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2.7
(2R)-2-hexanol
recombinant enzyme, pH and temperature not specified in the publication
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26.8
(2R)-2-hydroxypropyl-CoM
recombinant enzyme, pH and temperature not specified in the publication
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1.7
(2R)-2-octanol
recombinant enzyme, pH and temperature not specified in the publication
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1.1
(2R)-2-pentanol
recombinant enzyme, pH and temperature not specified in the publication
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2.2
(2S)-2-butanol
recombinant enzyme, pH and temperature not specified in the publication
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0.044
(2S)-2-hydroxypropyl-CoM
recombinant enzyme, pH and temperature not specified in the publication
2.9
(2S)-2-pentanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.29
2-(2-hydroxyethylthio)ethanesulfonate
recombinant enzyme, pH and temperature not specified in the publication
1.4
2-(2-ketopropylthio)ethanesulfonate
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pH 7.5, 30°C, mutant enzyme R152A
2.4
2-(2-ketopropylthio)ethanesulfonate
-
pH 7.5, 30°C, mutant enzyme R196A
15
2-(2-ketopropylthio)ethanesulfonate
-
pH 7.5, 30°C, mutant enzyme R209A
24.5
2-(2-ketopropylthio)ethanesulfonate
-
pH 7.5, 30°C, wild-type enzyme
27.9
2-(2-ketopropylthio)ethanesulfonate
-
pH 7.5, 30°C, mutant enzyme R203A
2.9
2-propanol
recombinant enzyme, pH and temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.003
(2R)-2-butanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.68
(2R)-2-heptanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.59
(2R)-2-hexanol
recombinant enzyme, pH and temperature not specified in the publication
-
262.75
(2R)-2-hydroxypropyl-CoM
recombinant enzyme, pH and temperature not specified in the publication
-
1.57
(2R)-2-octanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.055
(2R)-2-pentanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.007
(2S)-2-butanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.44
(2S)-2-hydroxypropyl-CoM
recombinant enzyme, pH and temperature not specified in the publication
0.019
(2S)-2-pentanol
recombinant enzyme, pH and temperature not specified in the publication
-
0.39
2-(2-hydroxyethylthio)ethanesulfonate
recombinant enzyme, pH and temperature not specified in the publication
0.0017
2-propanol
recombinant enzyme, pH and temperature not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.156
(2S)-2-hydroxypropyl-CoM
pH and temperature not specified in the publication, versus (2R)-2-hydroxypropyl-CoM
0.406
2-(2-methyl-2-hydroxypropylthio)-ethanesulfonate
pH and temperature not specified in the publication, versus (2R)-2-hydroxypropyl-CoM
-
0.156
2-(S)-hydroxypropyl-CoM
-
competitive inhibition with respect to 2-(R)-hydroxypropyl-CoM
26.7
ethanesulfonate
-
mixed-type inhibition with respect to 2-(R)-hydroxypropyl-CoM
2.25
mercaptoethanesulfonate
-
mixed-type inhibition with respect to 2-(R)-hydroxypropyl-CoM
147.8
methanesulfonate
-
mixed-type inhibition with respect to 2-(R)-hydroxypropyl-CoM
0.29
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
pH 7.5, 30°C
0.406
2-(2-methyl-2-hydroxypropylthio)ethanesulfonate
-
competitive inhibition with respect to 2-(R)-hydroxypropyl-CoM
2.25
CoM
pH and temperature not specified in the publication, competitive versus (2R)-2-hydroxypropyl-CoM
3.62
CoM
pH and temperature not specified in the publication, uncompetitive
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
metabolism of propylene depends on the presence of a linear megaplasmid, that encodes enzymes of alkene oxidation, epoxide carboxylation and CoM biosynthesis
brenda
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metabolism of propylene depends on the presence of a linear megaplasmid, that encodes enzymes of alkene oxidation, epoxide carboxylation and CoM biosynthesis
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brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
additional information
evolution
the enzyme belongs to the short-chain dehydrogenases/reductase (SDR) superfamily of enzymes. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity
evolution
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the enzyme belongs to the short-chain dehydrogenases/reductase (SDR) superfamily of enzymes. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity
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malfunction
substitution of R152 or R196 for alanine inhibits ethanesulfonate binding to the extent that its addition does not increase the EE of (S)-2-butanol produced by these mutants
malfunction
-
substitution of R152 or R196 for alanine inhibits ethanesulfonate binding to the extent that its addition does not increase the EE of (S)-2-butanol produced by these mutants
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metabolism
-
the bacterium produces R- and S-HPCDH, EC 1.1.1.268 and EC 1.1.1.269, simultaneously to facilitate transformation of R- and S-enantiomers of epoxy-propane to a common achiral product 2-ketopropyl-CoM
metabolism
(R)- and (S)-hydroxypropyl-coenzyme M dehydrogenase (R- and S-HPCDH), are part of a bacterial pathway of short-chain alkene and epoxide metabolism. R- and S-HPCDH act on different substrate enantiomers in a common pathway
metabolism
-
(R)- and (S)-hydroxypropyl-coenzyme M dehydrogenase (R- and S-HPCDH), are part of a bacterial pathway of short-chain alkene and epoxide metabolism. R- and S-HPCDH act on different substrate enantiomers in a common pathway
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additional information
-
structural basis for stereospecificity of R-HPCDH, comparison to S-HPCDH, EC 1.1.1.269, overview. Placement of catalytic residues within the active site of each enzyme is nearly identical, structural differences in the surrounding area provide each enzyme with a distinct substrate binding pocket
additional information
structure-function relationship, active site structure modeling and stereochemistry of reaction mechanism, overview. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity. Two arginine residues, R152 and R196, play a key role in substrate binding and stereoselectivity of enzyme R-HPCDH. R152 and R196 bind the sulfonate of 2-oxopropyl-CoM (2-KPC)
additional information
-
structure-function relationship, active site structure modeling and stereochemistry of reaction mechanism, overview. The C-terminal domains of SDR enzymes are responsible for imparting substrate specificity. Two arginine residues, R152 and R196, play a key role in substrate binding and stereoselectivity of enzyme R-HPCDH. R152 and R196 bind the sulfonate of 2-oxopropyl-CoM (2-KPC)
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